bioconductor.org "Spatial" keyword
cytoviewer 1.10.0
An interactive multi-channel image viewer for R6 versions - Latest release: 4 months ago - 8.49 thousand downloads total - 7 stars on GitHub - 1 maintainer
ggspavis 1.16.0
Visualization functions for spatial transcriptomics data10 versions - Latest release: 3 months ago - 1 dependent package - 17.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
visiumStitched 1.2.0
Enable downstream analysis of Visium capture areas stitched together with Fiji2 versions - Latest release: 4 months ago - 3.12 thousand downloads total - 4 stars on GitHub - 1 maintainer
mistyR 1.18.0
Multiview Intercellular SpaTial modeling framework7 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 44 stars on GitHub - 1 maintainer
FuseSOM 1.12.0
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets6 versions - Latest release: 3 months ago - 7.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
ggsc 1.8.0
Visualizing Single Cell and Spatial Transcriptomics7 versions - Latest release: 4 months ago - 7.67 thousand downloads total - 30 stars on GitHub - 1 maintainer
lisaClust 1.18.0
lisaClust: Clustering of Local Indicators of Spatial Association8 versions - Latest release: 3 months ago - 1 dependent package - 14.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
BulkSignalR 1.2.2
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...6 versions - Latest release: 4 days ago - 5.43 thousand downloads total - 1 stars on GitHub - 1 maintainer
SpotSweeper 1.6.0
Spatially-aware quality control for spatial transcriptomics8 versions - Latest release: 4 months ago - 6.88 thousand downloads total - 12 stars on GitHub - 1 maintainer
GeomxTools 3.14.0
NanoString GeoMx Tools9 versions - Latest release: 4 months ago - 3 dependent packages - 35.3 thousand downloads total - 1 maintainer
stJoincount 1.12.0
stJoincount - Join count statistic for quantifying spatial correlation between clusters6 versions - Latest release: 3 months ago - 7.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
tomoseqr 1.14.0
R Package for Analyzing Tomo-seq Data6 versions - Latest release: 3 months ago - 7.65 thousand downloads total - 1 maintainer
smoothclust 1.6.0
smoothclust6 versions - Latest release: 3 months ago - 5.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
7 versions - Latest release: 3 months ago - 36 dependent packages - 323 thousand downloads total - 54 stars on GitHub - 1 maintainer
SpatialExperiment 1.20.0
S4 Class for Spatially Resolved -omics Data7 versions - Latest release: 3 months ago - 36 dependent packages - 323 thousand downloads total - 54 stars on GitHub - 1 maintainer
SpatialOmicsOverlay 1.10.0
Spatial Overlay for Omic Data from Nanostring GeoMx Data7 versions - Latest release: 4 months ago - 7.25 thousand downloads total - 1 maintainer
betaHMM 1.6.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...6 versions - Latest release: 3 months ago - 5.26 thousand downloads total - 1 maintainer
spicyR 1.22.0
Spatial analysis of in situ cytometry data13 versions - Latest release: 4 months ago - 2 dependent packages - 20 thousand downloads total - 10 stars on GitHub - 1 maintainer
alabaster.sfe 1.2.0
Language agnostic on disk serialization of SpatialFeatureExperiment2 versions - Latest release: 4 months ago - 2.08 thousand downloads total - 0 stars on GitHub - 1 maintainer
pengls 1.16.0
Fit Penalised Generalised Least Squares models6 versions - Latest release: 3 months ago - 7.18 thousand downloads total - 0 stars on GitHub - 1 maintainer
miRspongeR 2.14.1
Identification and analysis of miRNA sponge regulation8 versions - Latest release: about 1 month ago - 1 dependent package - 12.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
imcRtools 1.16.0
Methods for imaging mass cytometry data analysis6 versions - Latest release: 4 months ago - 1 dependent package - 20.8 thousand downloads total - 27 stars on GitHub - 1 maintainer
SPIAT 1.12.1
Spatial Image Analysis of Tissues11 versions - Latest release: 6 days ago - 11.3 thousand downloads total - 24 stars on GitHub - 1 maintainer
shinyDSP 1.2.0
A Shiny App For Visualizing Nanostring GeoMx DSP Data3 versions - Latest release: 4 months ago - 3.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
nnSVG 1.14.0
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data10 versions - Latest release: 4 months ago - 2 dependent packages - 11.8 thousand downloads total - 22 stars on GitHub - 1 maintainer
escheR 1.10.0
Unified multi-dimensional visualizations with Gestalt principles7 versions - Latest release: 4 months ago - 2 dependent packages - 9.14 thousand downloads total - 7 stars on GitHub - 1 maintainer
mitology 1.2.0
Study of mitochondrial activity from RNA-seq data2 versions - Latest release: 4 months ago - 3 thousand downloads total - 2 stars on GitHub - 1 maintainer
spatialHeatmap 2.16.3
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions16 versions - Latest release: about 1 month ago - 14.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
scatterHatch 1.16.0
Creates hatched patterns for scatterplots6 versions - Latest release: 3 months ago - 7.16 thousand downloads total - 5 stars on GitHub - 1 maintainer
Banksy 1.6.0
Spatial transcriptomic clustering4 versions - Latest release: 4 months ago - 14.1 thousand downloads total - 123 stars on GitHub - 1 maintainer
MoleculeExperiment 1.10.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data9 versions - Latest release: 4 months ago - 7.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
SpotClean 1.12.1
SpotClean adjusts for spot swapping in spatial transcriptomics data9 versions - Latest release: 7 days ago - 9.82 thousand downloads total - 34 stars on GitHub - 1 maintainer
clustSIGNAL 1.2.0
ClustSIGNAL: a spatial clustering method2 versions - Latest release: 4 months ago - 2.77 thousand downloads total - 6 stars on GitHub - 1 maintainer
SpatialFeatureExperiment 1.12.1
Integrating SpatialExperiment with Simple Features in sf13 versions - Latest release: 4 months ago - 1 dependent package - 17.1 thousand downloads total - 57 stars on GitHub - 1 maintainer
tpSVG 1.6.0
Thin plate models to detect spatially variable genes5 versions - Latest release: 4 months ago - 4.86 thousand downloads total - 2 stars on GitHub - 1 maintainer
HuBMAPR 1.4.0
Interface to 'HuBMAP'7 versions - Latest release: 4 months ago - 3.94 thousand downloads total - 3 stars on GitHub - 1 maintainer
BatchSVG 1.2.0
Identify Batch-Biased Features in Spatially Variable Genes2 versions - Latest release: 4 months ago - 2.83 thousand downloads total - 3 stars on GitHub - 1 maintainer
Voyager 1.12.0
From geospatial to spatial omics6 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 96 stars on GitHub - 1 maintainer
standR 1.14.0
Spatial transcriptome analyses of Nanostring's DSP data in R6 versions - Latest release: 4 months ago - 12.1 thousand downloads total - 22 stars on GitHub - 1 maintainer
jazzPanda 1.2.0
Finding spatially relevant marker genes in image based spatial transcriptomics data4 versions - Latest release: 3 months ago - 3.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
HiCPotts 1.0.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C1 version - Latest release: 4 months ago - 799 downloads total - 0 stars on GitHub - 1 maintainer
simpleSeg 1.12.0
A package to perform simple cell segmentation10 versions - Latest release: 3 months ago - 9.69 thousand downloads total - 0 stars on GitHub - 1 maintainer
concordexR 1.10.0
Identify Spatial Homogeneous Regions with concordex6 versions - Latest release: 4 months ago - 7.02 thousand downloads total - 10 stars on GitHub - 1 maintainer
SPOTlight 1.14.0
`SPOTlight`: Spatial Transcriptomics Deconvolution10 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 199 stars on GitHub - 1 maintainer
SpaceMarkers 2.0.0
Spatial Interaction Markers4 versions - Latest release: 4 months ago - 4.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
scider 1.8.0
Spatial cell-type inter-correlation by density in R5 versions - Latest release: 3 months ago - 6.43 thousand downloads total - 7 stars on GitHub - 1 maintainer
SpaceTrooper 1.0.1
SpaceTrooper performs Quality Control analysis of Image-Based spatial2 versions - Latest release: about 2 months ago - 1.8 thousand downloads total - 8 stars on GitHub - 1 maintainer
spoon 1.6.0
Address the Mean-variance Relationship in Spatial Transcriptomics Data5 versions - Latest release: 3 months ago - 4.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
smoppix 1.2.2
Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index4 versions - Latest release: 18 days ago - 3 thousand downloads total - 1 stars on GitHub - 1 maintainer
CatsCradle 1.4.2
This package provides methods for analysing spatial transcriptomics data and for discovering gene...5 versions - Latest release: about 1 month ago - 4.24 thousand downloads total - 3 stars on GitHub - 1 maintainer
SpatialExperimentIO 1.2.0
Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object2 versions - Latest release: 4 months ago - 3.81 thousand downloads total - 16 stars on GitHub - 1 maintainer
spARI 1.0.0
Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering1 version - Latest release: 4 months ago - 973 downloads total - 1 maintainer
RegionalST 1.8.0
Investigating regions of interest and performing regional cell type-specific analysis with spatia...7 versions - Latest release: 3 months ago - 5.29 thousand downloads total - 1 maintainer
CTSV 1.12.0
Identification of cell-type-specific spatially variable genes accounting for excess zeros6 versions - Latest release: 4 months ago - 7.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
spacexr 1.2.0
SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics2 versions - Latest release: 4 months ago - 6.11 thousand downloads total - 3 stars on GitHub - 1 maintainer
OSTA.data 1.2.1
OSTA book data2 versions - Latest release: 3 months ago - 3.74 thousand downloads total - 2 stars on GitHub - 1 maintainer
scFeatures 1.10.9
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome predic...8 versions - Latest release: 19 days ago - 6.72 thousand downloads total - 14 stars on GitHub - 1 maintainer
CARDspa 1.2.1
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics3 versions - Latest release: 19 days ago - 3.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpaNorm 1.4.0
Spatially-aware normalisation for spatial transcriptomics data3 versions - Latest release: 3 months ago - 4.11 thousand downloads total - 13 stars on GitHub - 1 maintainer
signifinder 1.12.0
Collection and implementation of public transcriptional cancer signatures7 versions - Latest release: 4 months ago - 6.42 thousand downloads total - 9 stars on GitHub - 1 maintainer
Statial 1.12.0
A package to identify changes in cell state relative to spatial associations10 versions - Latest release: 4 months ago - 8.71 thousand downloads total - 6 stars on GitHub - 1 maintainer
hoodscanR 1.2.0
Spatial cellular neighbourhood scanning in R2 versions - Latest release: almost 2 years ago - 2.42 thousand downloads total - 9 stars on GitHub - 1 maintainer
scDesign3 1.8.0
A unified framework of realistic in silico data generation and statistical model inference for si...6 versions - Latest release: 4 months ago - 6.61 thousand downloads total - 105 stars on GitHub - 1 maintainer
spatialSimGP 1.4.0
Simulate Spatial Transcriptomics Data with the Mean-variance Relationship3 versions - Latest release: 4 months ago - 3.12 thousand downloads total - 0 stars on GitHub - 1 maintainer
knowYourCG 1.6.3
Functional analysis of DNA methylome datasets7 versions - Latest release: about 1 month ago - 5.64 thousand downloads total - 7 stars on GitHub - 1 maintainer
tidySpatialExperiment 1.6.2
SpatialExperiment with tidy principles8 versions - Latest release: 2 months ago - 6.26 thousand downloads total - 8 stars on GitHub - 1 maintainer
spatialFDA 1.2.0
A Tool for Spatial Multi-sample Comparisons2 versions - Latest release: 4 months ago - 3.37 thousand downloads total - 4 stars on GitHub - 1 maintainer
spaSim 1.12.0
Spatial point data simulator for tissue images6 versions - Latest release: 4 months ago - 7.21 thousand downloads total - 2 stars on GitHub - 1 maintainer
SEraster 1.2.0
Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis2 versions - Latest release: 3 months ago - 2.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
SpatialDecon 1.20.1
Deconvolution of mixed cells from spatial and/or bulk gene expression data8 versions - Latest release: 21 days ago - 1 dependent package - 17.8 thousand downloads total - 27 stars on GitHub - 1 maintainer
poem 1.2.0
POpulation-based Evaluation Metrics3 versions - Latest release: 4 months ago - 2.58 thousand downloads total - 8 stars on GitHub - 1 maintainer
sosta 1.2.0
A package for the analysis of anatomical tissue structures in spatial omics data3 versions - Latest release: 4 months ago - 3.47 thousand downloads total - 4 stars on GitHub - 1 maintainer
VisiumIO 1.6.3
Import Visium data from the 10X Space Ranger pipeline6 versions - Latest release: 3 months ago - 7.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
DESpace 2.2.2
DESpace: a framework to discover spatially variable genes and differential spatial patterns acros...8 versions - Latest release: 2 months ago - 7.95 thousand downloads total - 6 stars on GitHub - 1 maintainer
retrofit 1.10.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics6 versions - Latest release: 4 months ago - 6.08 thousand downloads total - 3 stars on GitHub - 1 maintainer
SVP 1.2.1
Predicting cell states and their variability in single-cell or spatial omics data4 versions - Latest release: 3 months ago - 3.66 thousand downloads total - 12 stars on GitHub - 1 maintainer
sccomp 2.2.0
Differential Composition and Variability Analysis for Single-Cell Data6 versions - Latest release: 3 months ago - 10.3 thousand downloads total - 112 stars on GitHub - 1 maintainer
tomoda 1.20.0
Tomo-seq data analysis6 versions - Latest release: 4 months ago - 8.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
stPipe 1.0.1
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics2 versions - Latest release: 3 months ago - 1.23 thousand downloads total - 4 stars on GitHub - 1 maintainer
XeniumIO 1.2.0
Import and represent Xenium data from the 10X Xenium Analyzer2 versions - Latest release: 3 months ago - 2.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
STdeconvolve 1.12.0 removed
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data5 versions - Latest release: 10 months ago - 7.67 thousand downloads total - 1 maintainer
Related Keywords
Software
80
Transcriptomics
52
SingleCell
49
GeneExpression
43
Visualization
19
DataImport
18
RNASeq
16
Clustering
14
Sequencing
11
ImmunoOncology
10
Infrastructure
8
DataRepresentation
8
StatisticalMethod
8
CellBasedAssays
7
QualityControl
7
spatial-transcriptomics
7
DimensionReduction
6
DifferentialExpression
6
r
6
Preprocessing
6
Regression
6
BiomedicalInformatics
6
Transcription
5
rstats
5
bioconductor
5
CellBiology
5
GeneTarget
4
Microarray
4
Bayesian
4
single-cell
4
Classification
3
Normalization
3
Proteomics
3
spatial-omics
3
bioconductor-package
3
spatial
3
spatial-statistics
2
visualization
2
ExperimentHubSoftware
2
Survival
2
r-package
2
GenomeAnnotation
2
MethylationArray
2
HiddenMarkovModel
2
GO
2
DNAMethylation
2
Reactome
2
ATACSeq
2
KEGG
2
FeatureExtraction
2
Network
2
u24ca289073
2
genomics
2
ProprietaryPlatforms
2
GraphAndNetwork
2
batch-effect
1
exploratory-data-analysis
1
BatchEffect
1
rstudio
1
random-effects
1
unwanted-variation
1
eda
1
omics
1
hubmap
1
proportions
1
esda
1
client
1
multilevel
1
SequenceMatching
1
spatial-data-analysis
1
spatial-analysis
1
GeneSetEnrichment
1
Epigenetics
1
ReportWriting
1
GeneSignaling
1
Genetics
1
FlowCytometry
1
Metagenomics
1
BiologicalQuestion
1
batch-correction
1
bayesian
1
PeakDetection
1
GenomeWideAssociation
1
composition
1
cytof
1
FunctionalGenomics
1
differential-proportion
1
microbiome
1
transcriptomics
1
ExperimentalDesign
1
quality-control
1
ligand-recepotor
1
interactions
1
NetworkInference
1
multiview
1
molecular-biology
1
modular
1
machine-learning
1
intercellular
1
biology
1